CARACTERÍSTICAS DE UN PERIODISTA WEB

11.7.1.1. Test 1: starting list of n= 40 VS interacting miRNAs n = 291 Python Script 12: ‘PS12_Test_miRNA_1.py’

From the starting list of 40 miRNAs shown in the green box in the top far left of Figure 24, 13 miRNAs were found in the list of interacting miRNAs, and were written to the output file ‘starting_mirnas_IN_interacting.txt’. Shown in the bottom far left of Figure 24, these 13 miRNAs were: hsa-miR-141, hsa-miR-142- 3p, hsa-miR-145, hsa-miR-146a, hsa-miR-155, hsa-miR-17-5p, hsa-miR-196a, hsa- miR-21, hsa-miR-224, hsa-miR-298, hsa-miR-409-3p, hsa-miR-423-5p, hsa-miR- 516a-5p. The miRNA-gene interactions were written to the text file ‘starting_ mirnas_found_interactions.txt’.

Table 20: The 13/40 starting miRNAs - not yet verified in miRBase - which were found in the list of interacting miRNAs as output from the analysis of the genes’ list of interactions

13 miRNAs from starting list of n = 40 No. of Interactions Gene interactions hsa-miR-141 1 PTPRD hsa-miR-142-3p 2 C2, C4BPB hsa-miR-145 2 FSCN1, KRT7

hsa-miR-146a 4 IRAK1, MCPH1, STAT1, TRAF6

hsa-miR-155 3 CCND1, ETS1, MATR3

hsa-miR-17-5p 19 ARIH1, ATXN7, CCL1, CCND1, CDKN1A,

CTSA, DCBLD2, GNAS, IGFBP5, IRAK1, KAT2A, PTTG1, RBL1, RPL37, RPS27A, RPSA, SMAD4, SYNDIG1, TRA2B

hsa-miR-196a 1 HOXA7

hsa-miR-21 3 CDKN1A, FAM3C, HNRNPK

hsa-miR-224 1 API5

hsa-miR-298 1 CDKN1A

hsa-miR-409-3p 1 FGG

hsa-miR-423-5p 11 CCNI, DRAP1, HIST2H2BE, HOXA7,

MYBL2, NFKB2, PTTG1, RPL18A, SLC7A2, UBE2L3, YWHAZ hsa-miR-516a-5p 1 SULF1        

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For these 13 starting miRNAs, 50 interacting genes were found for the pooled list of associated- and differentially-expressed genes as shown in Table 20. From these 13 starting miRNAs, unverified in miRBase, hsa-miR-17-5p and hsa-miR- 423-5p had the most gene interactions in the two databases, interacting with 19 and 11 genes, respectively. The miRNAs from the starting list which were not found in the list of interacting miRNAs was written to the output file ‘starting_mirnas_NOT_ IN_interacting.txt’. These 27 miRNAs were: hsa-miR-112, hsa-miR-1224-3P, hsa-miR-1224-3p, hsa-miR-125a, hsa-miR-126, hsa-miR-142, hsa-miR-148a, hsa-miR-150, hsa-miR-17-92, hsa-miR-181, hsa-miR-182-96-183, hsa-miR-184, hsa-miR-189, hsa-miR-198, hsa-miR-23b, hsa-miR-299-3p, hsa-miR- 3148, hsa-miR-342, hsa-miR-371-5p, hsa-miR-383, hsa-miR-483-5p, hsa-miR-513- 5p, hsa-miR-61, hsa-miR-629, hsa-miR-638, hsa-miR-663, hsa-miR-78.

11.7.1.2. Test 2: Verified (==) and (=regex) VS interacting miRNAs Python Script 13: ‘PS13_Test_miRNA_2.py’

In this script, the miRNAs verified as a perfect string match in miRBase, and the miRNAs verified as a regular expression in miRBase were pooled. A total of 57 miRNAs - 13 found as an exact string match, and 44 regular expression matches, see step 1 and step 2 of miRNA verification in BioMart – were cross-analysed for being present in the list of 291 unique interacting miRNAs. By using the Python set() function, a unique set of miRNAs was created to remove any duplicate miRNA names. The list of 57 miRNAs, verified in BioMart, was reduced to 56 miRNAs. From this list of 56 unique miRNAs, 22 miRNAs were found in the list of interacting miRNAs, and were written to the output file ‘verified_mirnas_IN_ interacting.txt’, as shown in the bottom right of Figure 25. These 22 miRNAs were: hsa-miR-125a-5p, hsa-miR-126-3p, hsa-miR-141-3p, hsa-miR-142-3p, hsa- miR-145-5p, hsa-miR-146a-5p, hsa-miR-148a-3p, hsa-miR-155-5p, hsa-miR-17- 5p, hsa-miR-181a-5p, hsa-miR-181b-5p, hsa-miR-181c-5p, hsa-miR-196a-5p, hsa- miR-21-5p, hsa-miR-224-5p, hsa-miR-23b-3p, hsa-miR-298, hsa-miR-342-3p, hsa- miR-409-3p, hsa-miR-423-5p, hsa-miR-516a-5p, hsa-miR-629-5p. These

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interactions were written to the output file ‘verified_mirnas_found_ interactions.txt’, and the interactions are shown in Table 20.

Table 21: The 22/56 starting miRNAs, which were verified in miRBase, and were found in the list of interacting miRNAs as output from the analysis of the genes lists.

22 miRNAs from verified list (n = 56) No. of Interactions Gene interactions

hsa-miR-125a-5p 8 ATP5G2, CDKN1A, COL4A1, FERMT1,

LAMB1, MACF1, OTUB2, TNFAIP3

hsa-miR-516a-5p 1 SULF1

hsa-miR-141-3p 2 PTPRD, ZFPM2

hsa-miR-148a-3p 4 AMELX, CCNI, CYCS, MPP5

hsa-miR-196a-5p 9 CCND1, EPHA7, HOXA7, NAP1L4, RANBP9,

TAB2, TRA2B, TSPAN12, ZBTB24

hsa-miR-142-3p 4 C2, C4BPB, C2, C4BPB

hsa-miR-342-3p 2 ATXN7, FAM3C

hsa-miR-409-3p 1 FGG

hsa-miR-21-5p 20 ARID4A, CCR1, DDX46, EIF4A2, ELOVL4, FAM3C, FAM46A,

HNRNPK, MPP5, MYEF2, NETO2, PHACTR2, PLAT, RASGRP3, RUFY3, SYNE2, TCF21, TNFAIP3, ZNF587, ZNF667

hsa-miR-298 1 CDKN1A

hsa-miR-145-5p 8 CDKN1A, CTGF, FAM3C, FSCN1,

FZD7, KRT7, MMP1, STAT1

hsa-miR-629-5p 2 ATP5G2, HIST1H2AC

hsa-miR-17-5p 19 ARIH1, ATXN7, CCL1, CCND1, CDKN1A, CTSA, DCBLD2,

GNAS, IGFBP5, IRAK1, KAT2A, PTTG1, RBL1, RPL37, RPS27A, RPSA, SMAD4, SYNDIG1, TRA2B

hsa-miR-146a-5p 15 CDKN1A, ERBB4, IFI27, IFI44, IFI44L, IFIT1, IFIT3, IRAK1,

ISG15, OASL, OLFML2A, SMAD4, SPP1, STAT1, TRAF6

hsa-miR-181a-5p 10 GCNT1, H3F3B, HEY2, KAT2B, PRLR,

PTPN22, SIK2, TAB2, TCF21, TNIP1

hsa-miR-181b-5p 2 KAT2B, RPL18A

hsa-miR-23b-3p 7 ACTN4, CCT7, GHITM, HNRNPK,

RPS27A, SLC16A1, TAB2

hsa-miR-181c-5p 1 NOTCH4

hsa-miR-155-5p 35 CCND1, CDH6, CHAF1B, CLDN1, CTSA, DRAP1, ETS1,

FAM135A, FAM3C, GHITM, GNAS, HAX1, HSPA4L, IMPAD1, MAFB, MATR3, MECP2, MPP5, NCAPD2, PDE3A, PHF14, PPFIBP1, PPP2R2A, RBM22, RIF1, SLC35F2, SMAD4, SMARCE1, STIM1, SYNE2, TAB2, UGT8, VAV2, YWHAZ, ZNF273

hsa-miR-423-5p 11 CCNI, DRAP1, HIST2H2BE, HOXA7, MYBL2, NFKB2, PTTG1,

RPL18A, SLC7A2, UBE2L3, YWHAZ

hsa-miR-224-5p 2 API5, SMAD4

hsa-miR-126-3p 1 PGR

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For these 22 miRNAs verified for their existence as a record in miRBase, 165 interactions were found for the pooled list of associated- and differentially- expressed genes, as shown in Table 21. From these 22 miRNAs, hsa-miR-155-5p had the most interactions, regulating 35 genes. This miRNA was followed by hsa- miR-21-5p and hsa-miR-7-5p, which regulated 20 and 19 genes, respectively. The 34 miRNAs which were verified in miRBase, but were not found to interact with the SLE-associated genes were written to the text file, verified_mirnas_NOT_IN_interacting.txt. The miRNA IDs written to this file were: hsa-miR-1224-3p, hsa-miR-125a-3p, hsa-miR-126-5p, hsa-miR-141-5p, hsa-miR- 142-5p, hsa-miR-145-3p, hsa-miR-146a-3p, hsa-miR-148a-5p, hsa-miR-150-3p, hsa-miR-150-5p, hsa-miR-155-3p, hsa-miR-181a-2-3p, hsa-miR-181a-3p, hsa-miR- 181b-2-3p, hsa-miR-181b-3p, hsa-miR-181c-3p, hsa-miR-181d-3p, hsa-miR-181d- 5p, hsa-miR-184, hsa-miR-196a-3p, hsa-miR-198, hsa-miR-21-3p, hsa-miR-224- 3p, hsa-miR-23b-5p, hsa-miR-299-3p, hsa-miR-3148, hsa-miR-342-5p, hsa-miR- 383-3p, hsa-miR-383-5p, hsa-miR-483-5p, hsa-miR-629-3p, hsa-miR-638, hsa- miR-663a, hsa-miR-663b.

11.7.1.3. Test 3: Not verified (n=27) VS interacting miRNAs Python Script 14: ‘PS14_Test_miRNA_3.py’

The above script analysed 27 miRNAs (‘no_match_in_miRBase.txt’) which failed the verification step as an exact string match in the miRBase database. From this list of 27 unique miRNAs, seven miRNAs were found in the list of interacting miRNAs, as shown in the far bottom right of Figure 24, and were written to the output file ‘not_verified_mirnas_IN_interacting.txt’. These seven miRNAs were: hsa-miR-141, hsa-miR-145, hsa-miR-146a, hsa-miR-155, hsa-miR-196a, hsa-miR- 21, hsa-miR-224.

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Table 22: The 7/27 miRNAs - NOT verified in miRBase - which were found in the list of interacting miRNAs as output from the analysis of the genes lists.

7 miRNAs

from unverified list of n = 27

No. of Interactions Gene interactions hsa-miR-141 1 PTPRD hsa-miR-145 2 FSCN1, KRT7

hsa-miR-146a 4 IRAK1, MCPH1, STAT1, TRAF6

hsa-miR-155 3 CCND1, ETS1, MATR3

hsa-miR-196a 1 HOXA7

hsa-miR-21 3 CDKN1A, FAM3C, HNRNPK

hsa-miR-224 1 API5

The gene interactions for the seven miRNAs which failed verification in BioMart were written to the output file ‘not_verified_mirnas_found_interactions.txt’ and are reported in Table 22. For these seven miRNAs not found as a record in miRBase, 15 interactions were found for the pooled list of SLE-associated- and differentially-expressed genes. From these seven miRNAs, hsa-miR-146a had the most interactions, regulating four genes.

The remaining 20 miRNAs which were not found in the list of interacting miRNAs was written to the output file, ‘not_verified_mirnas_NOT_IN_interacting.txt’. These 20 miRNAs were: hsa-miR-112, hsa-miR-1224-3P, hsa-miR-125a, hsa-miR- 126, hsa-miR-142, hsa-miR-148a, hsa-miR-150, hsa-miR-17-92, hsa-miR-181, hsa- miR-182-96-183, hsa-miR-189, hsa-miR-23b, hsa-miR-342, hsa-miR-371-5p, hsa- miR-383, hsa-miR-513-5p, hsa-miR-61, hsa-miR-629, hsa-miR-663, hsa-miR-78.

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11.7.2. Cross-Analysis of Pooled Lupus-associated and Differentially-